1. Intro:

Given the high diversity in perturbations in this study, the data are a good candidate to perform Weighted Gene Correlation Network Analysis. We will focus on specific downstream targets of kinases, which will give us course grained groupings of sites. This should help us recognize pathway crosstalk even for well established kinase targets.

2. Data Used:

Meta data for this report are available in:

Corrected and imputed data can be found in:

3. Site correlations in HOG1

## 
## Call:
## lm(formula = coef ~ group + treatment, data = .)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -0.9811 -0.7115 -0.5304  0.7192  1.5355 
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   1.78699    0.39829   4.487 0.000167 ***
## groupgroup_2  1.63640    0.34851   4.695 9.94e-05 ***
## treatmentKC   0.04444    0.48781   0.091 0.928204    
## treatmentNC   0.05656    0.48781   0.116 0.908705    
## treatmentSO   0.22038    0.48781   0.452 0.655659    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.9126 on 23 degrees of freedom
## Multiple R-squared:  0.4921, Adjusted R-squared:  0.4037 
## F-statistic: 5.571 on 4 and 23 DF,  p-value: 0.002755

## # A tibble: 4 × 6
##   site          treatment  coef    p.value adj.p.value regulated
##   <chr>         <chr>     <dbl>      <dbl>       <dbl> <lgl>    
## 1 YLR113W_Y_176 CA        0.961 0.347        0.766     FALSE    
## 2 YLR113W_Y_176 KC        4.23  0.00000127   0.0000972 TRUE     
## 3 YLR113W_Y_176 NC        1.44  0.0955       0.460     FALSE    
## 4 YLR113W_Y_176 SO        3.65  0.0000272    0.00130   TRUE

5. WGCNA analysis of TORC1

## Warning: executing %dopar% sequentially: no parallel backend registered
##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
## 1      1   0.7850  1.820          0.871 159.000   164.000 220.00
## 2      2   0.0715  0.229          0.565  59.500    59.800 108.00
## 3      3   0.1920 -0.388          0.705  27.000    25.000  62.20
## 4      4   0.4250 -0.816          0.790  13.900    11.500  39.80
## 5      5   0.6050 -1.120          0.882   7.810     5.930  27.30
## 6      6   0.7060 -1.300          0.911   4.690     3.130  19.70
## 7      7   0.7750 -1.440          0.936   2.980     1.820  14.60
## 8      8   0.8220 -1.460          0.959   1.970     1.080  11.10
## 9      9   0.8350 -1.510          0.968   1.350     0.695   8.63
## 10    10   0.8550 -1.500          0.970   0.958     0.448   6.78
## Warning: Removed 1 rows containing missing values (geom_point).

##  ..cutHeight not given, setting it to 0.998  ===>  99% of the (truncated) height range in dendro.
##  ..done.
## dynamicColors
##      blue     brown      grey turquoise 
##       174       164        70       230

6. WGCNA analysis of the full TORC1 cascade

##    Power SFT.R.sq  slope truncated.R.sq mean.k. median.k. max.k.
## 1      1   0.5360  1.870          0.797  227.00   233.000 322.00
## 2      2   0.0715  0.274          0.631   82.30    82.500 151.00
## 3      3   0.1830 -0.466          0.689   36.60    34.400  86.20
## 4      4   0.4400 -0.923          0.822   18.50    15.800  54.90
## 5      5   0.6410 -1.210          0.913   10.20     7.810  37.60
## 6      6   0.7590 -1.340          0.942    6.07     4.130  26.90
## 7      7   0.8100 -1.440          0.948    3.81     2.260  19.90
## 8      8   0.8590 -1.480          0.969    2.50     1.340  15.00
## 9      9   0.8810 -1.470          0.979    1.71     0.830  11.70
## 10    10   0.8530 -1.540          0.943    1.21     0.525   9.36

##  ..cutHeight not given, setting it to 0.998  ===>  99% of the (truncated) height range in dendro.
##  ..done.
## dynamicColors
##     black      blue     brown     green      grey   magenta      pink       red 
##        44       171       140        58        63        23        27        52 
## turquoise    yellow 
##       287        69

## Scale for 'y' is already present. Adding another scale for 'y', which will
## replace the existing scale.

## Warning: Removed 23 rows containing missing values (geom_text).
## Removed 23 rows containing missing values (geom_text).

6. WGCNA analysis of PPZ1 targets

##    Power SFT.R.sq   slope truncated.R.sq mean.k. median.k. max.k.
## 1      1   0.1630  0.6390          0.386  55.000    56.700  80.40
## 2      2   0.0275  0.0972          0.568  23.300    23.900  41.80
## 3      3   0.1650 -0.2080          0.716  11.500    11.000  24.70
## 4      4   0.3690 -0.5640          0.646   6.370     5.750  15.80
## 5      5   0.5600 -0.7070          0.762   3.800     3.080  10.80
## 6      6   0.7490 -0.8080          0.837   2.420     1.800   7.66
## 7      7   0.8070 -0.8870          0.834   1.630     1.100   5.68
## 8      8   0.9040 -0.9210          0.967   1.150     0.740   4.37
## 9      9   0.9400 -0.9360          0.956   0.849     0.543   3.46
## 10    10   0.8290 -1.0200          0.797   0.651     0.410   2.82

##  ..cutHeight not given, setting it to 0.996  ===>  99% of the (truncated) height range in dendro.
##  ..done.
## dynamicColors
##      blue      grey turquoise 
##        66        42        73